C-Index (JSBML 1.1 API Specification)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

C

C_DOT - Static variable in class org.sbml.jsbml.math.compiler.HTMLFormula: Multiplication symbol “⋅”.
C_DOT - Static variable in class org.sbml.jsbml.util.compilers.HTMLFormula: Multiplication symbol “⋅”.
CallableSBase - Interface in org.sbml.jsbml: The interface CallableSBase represents an SBase that can be called in mathematical expressions, i.e., ASTNode, via its identifier.
canConvert(Class) - Method in class org.sbml.jsbml.xml.xstream.converter.MessageConverter
canConvert(Class) - Method in class org.sbml.jsbml.xml.xstream.converter.SBMLErrorConverter
CBO - Class in org.sbml.jsbml.ext.dyn: Methods for interacting with Cell Behavior Ontology (CBO) terms.
CBO() - Constructor for class org.sbml.jsbml.ext.dyn.CBO
cboTerm - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
ceiling(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
ceiling(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
ceiling(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
ceiling(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
ceiling(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
changedBy - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
ChangedMath - Class in org.sbml.jsbml.ext.req: Declares which package has modified the value or the mathematical meaning of an SBase and in which way.
ChangedMath() - Constructor for class org.sbml.jsbml.ext.req.ChangedMath: Creates an ChangedMath instance
ChangedMath(String) - Constructor for class org.sbml.jsbml.ext.req.ChangedMath: Creates a ChangedMath instance with an id.
ChangedMath(int, int) - Constructor for class org.sbml.jsbml.ext.req.ChangedMath: Creates a ChangedMath instance with a level and version.
ChangedMath(String, int, int) - Constructor for class org.sbml.jsbml.ext.req.ChangedMath: Creates a ChangedMath instance with an id, level, and version.
ChangedMath(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.req.ChangedMath: Creates a ChangedMath instance with an id, name, level, and version.
ChangedMath(ChangedMath) - Constructor for class org.sbml.jsbml.ext.req.ChangedMath: Clone constructor
changedMath - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
charge - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
charge - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysConstraint: This function is used to check if the given model doesn't violate the constraint specified by this object.
check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysMathCheck
check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionArrayDimCheck
check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionIDCheck
check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionSizeCheck
check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.IndexArrayDimCheck
check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.IndexAttributesCheck
check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.SBaseWithDimensionCheck
checkAndSetVariable(String) - Method in class org.sbml.jsbml.EventAssignment: Sets the variableID of this EventAssignment to 'variable'.
checkAndSetVariable(String) - Method in class org.sbml.jsbml.InitialAssignment: Sets the variableID of this InitialAssignment to 'variable'.
checkConsistency() - Method in class org.sbml.jsbml.SBMLDocument: Validates the SBMLDocument using the SBML.org online validator (http://sbml.org/validator/).
checkConsistency(String, Map<String, String>) - Static method in class org.sbml.jsbml.validator.SBMLValidator: Validates an SBML model using the SBML.org online validator (http://sbml.org/validator/).
checkConsistency(String) - Static method in class org.sbml.jsbml.validator.SBMLValidator: Parses the XML String returned by the libSBML online validator or web services.
checkContainsNumbersReferingToUnits(Node) - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser: Deprecated.

Recursively checks whether the given Node contains any numbers that refer to unit declarations.
checkPackages(SBMLDocument) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil: Checks the whole SBMLDocument, including all siblings, to make sure that the package version and namespace is set properly.
checkPackages(SBMLDocument, boolean, boolean) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil: Checks the whole SBMLDocument, including all siblings, to make sure that the package version and namespace is set properly.
checkPackages(SBase, List<String>, boolean, boolean) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil: Checks the given SBase, including all it's siblings, to make sure that the package version and namespace is set properly.
checkTerm(String) - Static method in class org.sbml.jsbml.ext.dyn.CBO: Checks the format of the given CBO string.
checkTerm(int) - Static method in class org.sbml.jsbml.SBO: Checks the format of the given SBO integer portion.
checkTerm(String) - Static method in class org.sbml.jsbml.SBO: Checks the format of the given SBO string.
checkVectorAssignment(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath
checkVectorMath(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath
chemicalFormula - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
childNode - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
children() - Method in class org.sbml.jsbml.AbstractTreeNode
children() - Method in class org.sbml.jsbml.math.ASTUnknown
className - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
clear() - Method in class org.sbml.jsbml.ListOf
clear() - Method in class org.sbml.jsbml.UnitDefinition: Removes all Unit elements from the list of Units in this object.
clear() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML: Sets all the variable of this object to null.
clear() - Method in class org.sbml.jsbml.xml.XMLAttributes: Clears (deletes) all attributes in this XMLAttributes object.
clear() - Method in class org.sbml.jsbml.xml.XMLNamespaces: Clears (deletes) all XML namespace declarations in this XMLNamespaces object.
clearAttributes() - Method in class org.sbml.jsbml.xml.XMLToken: Clears (deletes) all attributes in this XMLToken.
clearIdToVector() - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
clearListOfEventAssignments() - Method in class org.sbml.jsbml.Event: Remove all the EventAssignments of the listOfEventAssignments of this Event.
clearLog() - Method in class org.sbml.jsbml.SBMLErrorLog: Clears the log.
clearNamespaces() - Method in class org.sbml.jsbml.xml.XMLToken: Clears (deletes) all XML namespace declarations in the XMLNamespaces of this XMLToken.
clearUserObjects() - Method in class org.sbml.jsbml.AbstractTreeNode
clearUserObjects() - Method in class org.sbml.jsbml.math.ASTUnknown
clearUserObjects() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport: Removes all of the mappings from the map of user objects (optional operation).
clone() - Method in class org.sbml.jsbml.AbstractMathContainer
clone() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
clone() - Method in class org.sbml.jsbml.AbstractSBase
clone() - Method in class org.sbml.jsbml.AbstractTreeNode
clone() - Method in class org.sbml.jsbml.AlgebraicRule
clone() - Method in class org.sbml.jsbml.Annotation
clone() - Method in class org.sbml.jsbml.AssignmentRule
clone() - Method in class org.sbml.jsbml.ASTNode
clone() - Method in class org.sbml.jsbml.Compartment
clone() - Method in class org.sbml.jsbml.CompartmentType: Deprecated.
clone() - Method in class org.sbml.jsbml.Constraint
clone() - Method in class org.sbml.jsbml.Creator
clone() - Method in class org.sbml.jsbml.CVTerm
clone() - Method in class org.sbml.jsbml.Delay
clone() - Method in class org.sbml.jsbml.Event
clone() - Method in class org.sbml.jsbml.EventAssignment
clone() - Method in class org.sbml.jsbml.ExplicitRule
clone() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
clone() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin
clone() - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
clone() - Method in class org.sbml.jsbml.ext.arrays.Dimension: clones this class
clone() - Method in class org.sbml.jsbml.ext.arrays.Index: clones this class
clone() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin
clone() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin: clones this class
clone() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
clone() - Method in class org.sbml.jsbml.ext.comp.Deletion
clone() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition: clones this class
clone() - Method in class org.sbml.jsbml.ext.comp.ModelDefinition
clone() - Method in class org.sbml.jsbml.ext.comp.Port
clone() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy: clones this class
clone() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement: clones this class
clone() - Method in class org.sbml.jsbml.ext.comp.SBaseRef
clone() - Method in class org.sbml.jsbml.ext.comp.Submodel: clones this class
clone() - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin
clone() - Method in class org.sbml.jsbml.ext.distrib.DistribInput: clones this class
clone() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin
clone() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution: clones this class
clone() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty
clone() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin
clone() - Method in class org.sbml.jsbml.ext.dyn.DynElement
clone() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin
clone() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin
clone() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent
clone() - Method in class org.sbml.jsbml.ext.fbc.And
clone() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
clone() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
clone() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin
clone() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
clone() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: clones this class
clone() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct
clone() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation
clone() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef
clone() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives
clone() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator
clone() - Method in class org.sbml.jsbml.ext.fbc.Objective
clone() - Method in class org.sbml.jsbml.ext.fbc.Or
clone() - Method in class org.sbml.jsbml.ext.groups.Group
clone() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin
clone() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.
clone() - Method in class org.sbml.jsbml.ext.groups.Member
clone() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint: Deprecated.
clone() - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
clone() - Method in class org.sbml.jsbml.ext.layout.BoundingBox
clone() - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph
clone() - Method in class org.sbml.jsbml.ext.layout.CubicBezier
clone() - Method in class org.sbml.jsbml.ext.layout.Curve
clone() - Method in class org.sbml.jsbml.ext.layout.Dimensions
clone() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph
clone() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject
clone() - Method in class org.sbml.jsbml.ext.layout.Layout
clone() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin
clone() - Method in class org.sbml.jsbml.ext.layout.LineSegment
clone() - Method in class org.sbml.jsbml.ext.layout.Point
clone() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph
clone() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph
clone() - Method in class org.sbml.jsbml.ext.layout.SpeciesGlyph
clone() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
clone() - Method in class org.sbml.jsbml.ext.layout.TextGlyph
clone() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference
clone() - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.IntraSpeciesReaction: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin
clone() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin
clone() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
clone() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesType: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: clones this class
clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: clones this class
clone() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm
clone() - Method in class org.sbml.jsbml.ext.qual.Input
clone() - Method in class org.sbml.jsbml.ext.qual.Output
clone() - Method in class org.sbml.jsbml.ext.qual.QualConstants
clone() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
clone() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin
clone() - Method in class org.sbml.jsbml.ext.qual.Transition
clone() - Method in class org.sbml.jsbml.ext.render.ColorDefinition
clone() - Method in class org.sbml.jsbml.ext.render.Ellipse
clone() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation
clone() - Method in class org.sbml.jsbml.ext.render.GradientBase
clone() - Method in class org.sbml.jsbml.ext.render.GradientStop
clone() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D
clone() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D
clone() - Method in class org.sbml.jsbml.ext.render.Image
clone() - Method in class org.sbml.jsbml.ext.render.LinearGradient
clone() - Method in class org.sbml.jsbml.ext.render.LineEnding
clone() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation
clone() - Method in class org.sbml.jsbml.ext.render.Polygon
clone() - Method in class org.sbml.jsbml.ext.render.RadialGradient
clone() - Method in class org.sbml.jsbml.ext.render.Rectangle
clone() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
clone() - Method in class org.sbml.jsbml.ext.render.RenderCurve
clone() - Method in class org.sbml.jsbml.ext.render.RenderGroup
clone() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
clone() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin
clone() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin
clone() - Method in class org.sbml.jsbml.ext.render.RenderPoint
clone() - Method in class org.sbml.jsbml.ext.render.Style
clone() - Method in class org.sbml.jsbml.ext.render.Transformation
clone() - Method in class org.sbml.jsbml.ext.render.Transformation2D
clone() - Method in class org.sbml.jsbml.ext.req.ChangedMath: clones this class
clone() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin: clones this class
clone() - Method in interface org.sbml.jsbml.ext.SBasePlugin: Creates a new instance of SBasePlugin from this SBasePlugin.
clone() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
clone() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin
clone() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains
clone() - Method in class org.sbml.jsbml.ext.spatial.AdvectionCoefficient
clone() - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry
clone() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume
clone() - Method in class org.sbml.jsbml.ext.spatial.Boundary
clone() - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition
clone() - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping
clone() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent
clone() - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference: Deprecated.
clone() - Method in class org.sbml.jsbml.ext.spatial.CSGeometry
clone() - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation
clone() - Method in class org.sbml.jsbml.ext.spatial.CSGObject
clone() - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive
clone() - Method in class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive
clone() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation
clone() - Method in class org.sbml.jsbml.ext.spatial.CSGScale
clone() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator
clone() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation
clone() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient
clone() - Method in class org.sbml.jsbml.ext.spatial.Domain
clone() - Method in class org.sbml.jsbml.ext.spatial.DomainType
clone() - Method in class org.sbml.jsbml.ext.spatial.Geometry
clone() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint
clone() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry
clone() - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping
clone() - Method in class org.sbml.jsbml.ext.spatial.ParameterType
clone() - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry
clone() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject
clone() - Method in class org.sbml.jsbml.ext.spatial.PolygonObject: Deprecated.
clone() - Method in class org.sbml.jsbml.ext.spatial.SampledField
clone() - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry
clone() - Method in class org.sbml.jsbml.ext.spatial.SampledVolume
clone() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin
clone() - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin
clone() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin
clone() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints: clones this class
clone() - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin
clone() - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
clone() - Method in class org.sbml.jsbml.ext.spatial.SpatialSymbolReference
clone() - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent
clone() - Method in class org.sbml.jsbml.FunctionDefinition
clone() - Method in class org.sbml.jsbml.History
clone() - Method in class org.sbml.jsbml.InitialAssignment
clone() - Method in class org.sbml.jsbml.KineticLaw
clone() - Method in class org.sbml.jsbml.ListOf
clone() - Method in class org.sbml.jsbml.LocalParameter
clone() - Method in class org.sbml.jsbml.math.AbstractASTNode
clone() - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode
clone() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
clone() - Method in class org.sbml.jsbml.math.ASTBoolean
clone() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
clone() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
clone() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
clone() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
clone() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
clone() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
clone() - Method in class org.sbml.jsbml.math.ASTCnRealNode
clone() - Method in class org.sbml.jsbml.math.ASTConstantNumber
clone() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
clone() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
clone() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
clone() - Method in class org.sbml.jsbml.math.ASTDivideNode
clone() - Method in class org.sbml.jsbml.math.ASTFunction
clone() - Method in class org.sbml.jsbml.math.ASTHyperbolicNode
clone() - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
clone() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
clone() - Method in class org.sbml.jsbml.math.ASTLogicalOperatorNode
clone() - Method in class org.sbml.jsbml.math.ASTMinusNode
clone() - Method in interface org.sbml.jsbml.math.ASTNode2: Clone ASTNode2
clone() - Method in class org.sbml.jsbml.math.ASTNumber
clone() - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
clone() - Method in class org.sbml.jsbml.math.ASTPlusNode
clone() - Method in class org.sbml.jsbml.math.ASTPowerNode
clone() - Method in class org.sbml.jsbml.math.ASTQualifierNode
clone() - Method in class org.sbml.jsbml.math.ASTRelationalOperatorNode
clone() - Method in class org.sbml.jsbml.math.ASTRootNode
clone() - Method in class org.sbml.jsbml.math.ASTTimesNode
clone() - Method in class org.sbml.jsbml.math.ASTTrigonometricNode
clone() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
clone() - Method in class org.sbml.jsbml.math.ASTUnknown
clone() - Method in class org.sbml.jsbml.Model
clone() - Method in class org.sbml.jsbml.ModifierSpeciesReference
clone() - Method in class org.sbml.jsbml.ontology.Term
clone() - Method in class org.sbml.jsbml.ontology.Triple
clone() - Method in class org.sbml.jsbml.Parameter
clone() - Method in class org.sbml.jsbml.Priority
clone() - Method in class org.sbml.jsbml.QuantityWithUnit
clone() - Method in class org.sbml.jsbml.RateRule
clone() - Method in class org.sbml.jsbml.Reaction
clone() - Method in class org.sbml.jsbml.Rule
clone() - Method in interface org.sbml.jsbml.SBase: Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
clone() - Method in class org.sbml.jsbml.SBMLDocument
clone() - Method in class org.sbml.jsbml.SBMLReader
clone() - Method in class org.sbml.jsbml.SBMLWriter
clone() - Method in class org.sbml.jsbml.Species
clone() - Method in class org.sbml.jsbml.SpeciesReference
clone() - Method in class org.sbml.jsbml.SpeciesType: Deprecated.
clone() - Method in class org.sbml.jsbml.StoichiometryMath: Deprecated.
clone() - Method in class org.sbml.jsbml.Symbol
clone() - Method in class org.sbml.jsbml.Trigger
clone() - Method in class org.sbml.jsbml.Unit
clone() - Method in class org.sbml.jsbml.UnitDefinition
clone() - Method in class org.sbml.jsbml.util.ListOfWithName
clone() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
clone() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
clone() - Method in class org.sbml.jsbml.util.ValuePair
clone() - Method in class org.sbml.jsbml.xml.XMLAttributes: Creates and returns a deep copy of this XMLAttributes set.
clone() - Method in class org.sbml.jsbml.xml.XMLNamespaces: Creates and returns a deep copy of this XMLNamespaces list.
clone() - Method in class org.sbml.jsbml.xml.XMLNode
clone() - Method in class org.sbml.jsbml.xml.XMLToken
clone() - Method in class org.sbml.jsbml.xml.XMLTriple: Creates and returns a deep copy of this XMLTriple set.
CLOSE_PAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants: RegularExpression Id.
CLOSE_PAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants: RegularExpression Id.
CLOSE_PAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants: RegularExpression Id.
CLOSE_PAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants: RegularExpression Id.
CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants: RegularExpression Id.
CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants: RegularExpression Id.
CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants: RegularExpression Id.
CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants: RegularExpression Id.
CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants: RegularExpression Id.
CobraFormulaParser - Class in org.sbml.jsbml.text.parser: Class used to parse infix mathematical formula written by the COBRA toolbox and returns a representation of it as an Abstract Syntax Tree (AST).
CobraFormulaParser(InputStream) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser: Constructor with InputStream.
CobraFormulaParser(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser: Constructor with InputStream and supplied encoding
CobraFormulaParser(Reader) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser: Constructor.
CobraFormulaParser(CobraFormulaParserTokenManager) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser: Constructor with generated Token Manager.
CobraFormulaParserConstants - Interface in org.sbml.jsbml.text.parser: Token literal values and constants.
CobraFormulaParserTokenManager - Class in org.sbml.jsbml.text.parser: Token Manager.
CobraFormulaParserTokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager: Constructor.
CobraFormulaParserTokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager: Constructor.
CobraUtil - Class in org.sbml.jsbml.util: Contains some useful methods to manipulate 'COBRA SBML'
CobraUtil() - Constructor for class org.sbml.jsbml.util.CobraUtil
coefficient - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
colorbox(String, Object) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
colorbox(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
ColorDefinition - Class in org.sbml.jsbml.ext.render
ColorDefinition() - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition: Creates an ColorDefinition instance
ColorDefinition(String) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition: Creates a ColorDefinition instance with an id.
ColorDefinition(String, Color) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition: Creates a ColorDefinition instance with an id.
ColorDefinition(int, int) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition: Creates a ColorDefinition instance with a level and version.
ColorDefinition(String, int, int) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition: Creates a ColorDefinition instance with an id, level, and version.
ColorDefinition(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition: Creates a ColorDefinition instance with an id, name, level, and version.
ColorDefinition(ColorDefinition) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition: Clone constructor
colorDefiniton - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
compareTo(Term) - Method in class org.sbml.jsbml.ontology.Term
compareTo(Triple) - Method in class org.sbml.jsbml.ontology.Triple
compareTo(L, V) - Method in class org.sbml.jsbml.util.ValuePair: Convenient method to compare two values to this ValuePair.
compareTo(ValuePair<L, V>) - Method in class org.sbml.jsbml.util.ValuePair
COMPARISON - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants: RegularExpression Id.
COMPARISON - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants: RegularExpression Id.
COMPARISON - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants: RegularExpression Id.
COMPARISON - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants: RegularExpression Id.
COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants: RegularExpression Id.
COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants: RegularExpression Id.
COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants: RegularExpression Id.
COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants: RegularExpression Id.
COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants: RegularExpression Id.
Compartment - Class in org.sbml.jsbml: Represents the compartment in a model, i.e., a variable element with name, identifier, unit, and value that may change during a simulation.
Compartment() - Constructor for class org.sbml.jsbml.Compartment: Creates a Compartment instance.
Compartment(Compartment) - Constructor for class org.sbml.jsbml.Compartment: Creates a Compartment instance from a given compartment.
Compartment(int, int) - Constructor for class org.sbml.jsbml.Compartment: Creates a Compartment instance from a level and version.
Compartment(String) - Constructor for class org.sbml.jsbml.Compartment: Creates a Compartment instance with the given id.
Compartment(String, int, int) - Constructor for class org.sbml.jsbml.Compartment: Creates a Compartment instance from an id, level and version.
Compartment(String, String, int, int) - Constructor for class org.sbml.jsbml.Compartment: Creates a Compartment instance from an id, name, level and version.
compartment - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
compartment - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
compartment - Static variable in class org.sbml.jsbml.ext.qual.QualConstants
compartment - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
compartment - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
CompartmentalizedSBase - Interface in org.sbml.jsbml
CompartmentGlyph - Class in org.sbml.jsbml.ext.layout: The CompartmentGlyph class is derived from GraphicalObject and inherits its attributes.
CompartmentGlyph() - Constructor for class org.sbml.jsbml.ext.layout.CompartmentGlyph
CompartmentGlyph(CompartmentGlyph) - Constructor for class org.sbml.jsbml.ext.layout.CompartmentGlyph
CompartmentGlyph(int, int) - Constructor for class org.sbml.jsbml.ext.layout.CompartmentGlyph
CompartmentGlyph(String) - Constructor for class org.sbml.jsbml.ext.layout.CompartmentGlyph
CompartmentGlyph(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.CompartmentGlyph
compartmentGlyph - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
CompartmentMapping - Class in org.sbml.jsbml.ext.spatial
CompartmentMapping() - Constructor for class org.sbml.jsbml.ext.spatial.CompartmentMapping
CompartmentMapping(CompartmentMapping) - Constructor for class org.sbml.jsbml.ext.spatial.CompartmentMapping
CompartmentMapping(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CompartmentMapping
CompartmentMapping(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CompartmentMapping
compartmentMapping - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CompartmentReference - Class in org.sbml.jsbml.ext.multi
CompartmentReference() - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference: Creates an CompartmentReference instance
CompartmentReference(CompartmentReference) - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference: Clone constructor
CompartmentReference(int, int) - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference: Creates a CompartmentReference instance with a level and version.
CompartmentReference(String) - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference: Creates a CompartmentReference instance with an id.
CompartmentReference(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference: Creates a CompartmentReference instance with an id, level, and version.
CompartmentReference(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference: Creates a CompartmentReference instance with an id, name, level, and version.
compartmentReference - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
CompartmentType - Class in org.sbml.jsbml: Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
CompartmentType() - Constructor for class org.sbml.jsbml.CompartmentType: Deprecated.
CompartmentType(CompartmentType) - Constructor for class org.sbml.jsbml.CompartmentType: Deprecated.
CompartmentType(int, int) - Constructor for class org.sbml.jsbml.CompartmentType: Deprecated.
CompartmentType(String) - Constructor for class org.sbml.jsbml.CompartmentType: Deprecated.
CompartmentType(String, int, int) - Constructor for class org.sbml.jsbml.CompartmentType: Deprecated.
CompartmentType(String, String, int, int) - Constructor for class org.sbml.jsbml.CompartmentType: Deprecated.
compartmentType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
compartmentType - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
CompConstants - Class in org.sbml.jsbml.ext.comp: Contains some constants related to the comp package.
CompConstants() - Constructor for class org.sbml.jsbml.ext.comp.CompConstants
compile(ASTNodeCompiler) - Method in class org.sbml.jsbml.ASTNode: Compiles this ASTNode and returns the result.
compile(Compartment) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
compile(double, int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
compile(double, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
compile(int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
compile(CallableSBase) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
compile(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
compile(Compartment) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
compile(double, int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
compile(double, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
compile(int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
compile(CallableSBase) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
compile(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
compile(Compartment) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
compile(double, int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
compile(double, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
compile(int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
compile(CallableSBase) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
compile(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTBoolean
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCiNumberNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnNumberNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnRationalNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnRealNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTConstantNumber
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTDivideNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTFunction
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTHyperbolicNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTLogicalOperatorNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTMinusNode
compile(ASTNode2Compiler) - Method in interface org.sbml.jsbml.math.ASTNode2: Compiles this ASTNode2 and returns the result.
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTPlusNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTPowerNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTQualifierNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTRelationalOperatorNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTRootNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTTimesNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTTrigonometricNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTUnknown
compile(Compartment) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
compile(double, int, String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler: Creates an ASTNode2Value that represents a real number in scientific notation, i.e., mantissa * 10^exponent, and the given units.
compile(double, String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
compile(int, String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
compile(CallableSBase) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
compile(String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler: A compiler will also have to deal with a name.
compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
compile(double, int, String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
compile(double, String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
compile(int, String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
compile(String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
compile(double, int, String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
compile(double, String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
compile(int, String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
compile(String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler: This method returns the correct LaTeX expression for a function which returns the size of a compartment.
compile(double, int, String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
compile(double, String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
compile(int, String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
compile(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
compile(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler: Compiles this ASTNode2 and produce an XMLStreamWriter representing this node in mathML.
compile(boolean) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler: Compile boolean values
compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
compile(double, int, String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
compile(double, String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
compile(int, String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
compile(String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
compile(Compartment) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
compile(double, int, String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler: Creates an ASTNodeValue that represents a real number in scientific notation, i.e., mantissa * 10^exponent, and the given units.
compile(double, String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
compile(int, String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
compile(CallableSBase) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
compile(String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler: A compiler will also have to deal with a name.
compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
compile(double, String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
compile(int, String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
compile(String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
compile(double, String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
compile(int, String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
compile(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler: This method returns the correct LaTeX expression for a function which returns the size of a compartment.
compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
compile(double, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
compile(int, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
compile(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
compile(double, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
compile(int, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
compile(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
compile(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler: Compiles this ASTNode and produce an XMLStreamWriter representing this node in mathML.
compile(boolean) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler: Compile boolean values
compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
compile(double, String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
compile(int, String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
compile(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
complementA - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
complementB - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CompModelPlugin - Class in org.sbml.jsbml.ext.comp: The extended Model class adds two lists, one for holding Submodels and the other for holding Ports.
CompModelPlugin(CompModelPlugin) - Constructor for class org.sbml.jsbml.ext.comp.CompModelPlugin: Creates a new CompModelPlugin instance that is a copy of the current CompModelPlugin.
CompModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.comp.CompModelPlugin: Creates a new CompModelPlugin instance, associated with the given Model
component - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
components - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
componentsLength - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
componentType - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CompParser - Class in org.sbml.jsbml.xml.parsers: A CompParser is used to parse the comp extension package elements and attributes.
CompParser() - Constructor for class org.sbml.jsbml.xml.parsers.CompParser
compression - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CompressionKind - Enum in org.sbml.jsbml.ext.spatial: This enum type was created following the specifications defined in Spatial Package v0.90.
CompSBasePlugin - Class in org.sbml.jsbml.ext.comp: The CompSBasePlugin class extends the SBase class by adding an optional ListOfReplacedElements child and a single optional ReplacedBy child.
CompSBasePlugin() - Constructor for class org.sbml.jsbml.ext.comp.CompSBasePlugin: Creates an CompSBasePlugin instance
CompSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.comp.CompSBasePlugin: Creates a CompSBasePlugin instance with a level and version.
CompSBasePlugin(CompSBasePlugin) - Constructor for class org.sbml.jsbml.ext.comp.CompSBasePlugin: Clone constructor
CompSBMLDocumentPlugin - Class in org.sbml.jsbml.ext.comp: The top level of an SBMLDocument is a container whose structure is defined by the object class SBML in the SBML Level 3 Version 1 Core specification.
CompSBMLDocumentPlugin(SBMLDocument) - Constructor for class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
CompSBMLDocumentPlugin(CompSBMLDocumentPlugin) - Constructor for class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
concat(Object...) - Static method in class org.sbml.jsbml.util.StringTools: This method concatenates two or more Object Strings (obtained by calling Object.toString() if the current Object is not null) into a new StringBuffer.
concatStringBuilder(Object...) - Static method in class org.sbml.jsbml.util.StringTools: This method concatenates two or more Object Strings (obtained by calling Object.toString() if the current Object is not null) into a new StringBuilder.
connex - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
constant - Static variable in class org.sbml.jsbml.ext.qual.QualConstants
constant - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
CONSTANT_E - Variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
CONSTANT_E - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
CONSTANT_FALSE - Variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
CONSTANT_FALSE - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
CONSTANT_PI - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler: The constant pi
CONSTANT_PI - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler: The constant pi
CONSTANT_TRUE - Variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
CONSTANT_TRUE - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Constraint - Class in org.sbml.jsbml: Represents the constraint XML element of a SBML file.
Constraint() - Constructor for class org.sbml.jsbml.Constraint: Creates a Constraint instance.
Constraint(ASTNode, int, int) - Constructor for class org.sbml.jsbml.Constraint: Creates a Constraint instance from an ASTNode, a level and a version.
Constraint(Constraint) - Constructor for class org.sbml.jsbml.Constraint: Creates a Constraint instance from a given Constraint.
Constraint(int, int) - Constructor for class org.sbml.jsbml.Constraint: Creates a Constraint instance from a level and a version.
containedSpeciesType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
contains(Object) - Method in class org.sbml.jsbml.ListOf
containsAll(Collection<?>) - Method in class org.sbml.jsbml.ListOf
containsCompartment(String) - Method in class org.sbml.jsbml.Model: Returns true if this model contains a reference to a Compartment with the given identifier.
containsFunctionDefinition(String) - Method in class org.sbml.jsbml.Model: Returns true if this model contains a reference to a FunctionDefinition with the given identifier.
containsGlyph(Compartment) - Method in class org.sbml.jsbml.ext.layout.Layout
containsGlyph(Reaction) - Method in class org.sbml.jsbml.ext.layout.Layout
containsGlyph(Species) - Method in class org.sbml.jsbml.ext.layout.Layout
containsMetaId(String) - Method in class org.sbml.jsbml.SBMLDocument: A check to see whether elements have been registered to this SBMLDocument with the given meta identifier.
containsParameter(String) - Method in class org.sbml.jsbml.Model: Returns true if this model contains a reference to a Parameter with the given identifier.
containsQualitativeSpecies(QualitativeSpecies) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Returns true if qs is already part of this QualModelPlugin
containsQuantity(Quantity) - Method in class org.sbml.jsbml.Model: Returns true if this Model contains a reference to the given Quantity.
containsReaction(String) - Method in class org.sbml.jsbml.Model: Returns true if this Model contains a reference to the given Reaction.
containsSpecies(String) - Method in class org.sbml.jsbml.Model: Returns true if this Model contains a reference to the given Species.
containsUndeclaredUnits() - Method in class org.sbml.jsbml.AbstractMathContainer
containsUndeclaredUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
containsUndeclaredUnits() - Method in class org.sbml.jsbml.ASTNode: Returns true or false depending on whether this ASTNode refers to elements such as parameters or numbers with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.jsbml.Compartment
containsUndeclaredUnits() - Method in class org.sbml.jsbml.Event: Deprecated.
containsUndeclaredUnits() - Method in class org.sbml.jsbml.ext.arrays.Dimension
containsUndeclaredUnits() - Method in class org.sbml.jsbml.ext.qual.Input
containsUndeclaredUnits() - Method in class org.sbml.jsbml.ext.qual.Output
containsUndeclaredUnits() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent
containsUndeclaredUnits() - Method in class org.sbml.jsbml.math.ASTCiNumberNode: Returns true or false depending on whether this ASTCiNumberNode refers to elements such as parameters or numbers with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value: Flag to indicate whether or not units have been fully declared for this value.
containsUndeclaredUnits() - Method in class org.sbml.jsbml.Reaction
containsUndeclaredUnits() - Method in interface org.sbml.jsbml.SBaseWithDerivedUnit: Returns true or false depending on whether this SBaseWithDerivedUnit refers to elements such as parameters or numbers with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.jsbml.Species
containsUndeclaredUnits() - Method in class org.sbml.jsbml.SpeciesReference
containsUndeclaredUnits() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue: Flag to indicate whether or not units have been fully declared for this value.
containsUniqueNamedSBase(String) - Method in class org.sbml.jsbml.Model: Returns true if this Model contains a reference to the given UniqueNamedSBase.
containsUnitDefinition(String) - Method in class org.sbml.jsbml.Model: Returns true if this Model contains a reference to the given UnitDefinition.
containsUserObjectKey(Object) - Method in class org.sbml.jsbml.AbstractTreeNode
containsUserObjectKey(Object) - Method in class org.sbml.jsbml.math.ASTUnknown
containsUserObjectKey(Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
conversionFactor - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
conversionFactor - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
convert(SBMLDocument) - Static method in class org.sbml.jsbml.ext.arrays.flattening.ArraysFlattening: This method flattens out arrays objects of a given SBMLDocument.
convertAlias2SBO(String) - Static method in class org.sbml.jsbml.SBO: Returns an SBO id corresponding to the given alias.
convertModel(T) - Method in interface org.sbml.jsbml.SBMLInputConverter: Takes a model in an arbitrary (but type-secure) format and delivers a corresponding JSBML-compliant model.
convertSBMLDocument(File) - Method in interface org.sbml.jsbml.SBMLInputConverter
convertSBMLDocument(String) - Method in interface org.sbml.jsbml.SBMLInputConverter
convertSBO2Alias(int) - Static method in class org.sbml.jsbml.SBO: Returns an alias corresponding to the given SBO id.
convertStringToXMLNode(String) - Static method in class org.sbml.jsbml.xml.XMLNode: Returns an XMLNode which is derived from a String containing XML content.
convertStringToXMLNode(String, XMLNamespaces) - Static method in class org.sbml.jsbml.xml.XMLNode: Returns an XMLNode which is derived from a string containing XML content.
convertToGMT(Date) - Method in class org.sbml.jsbml.xml.stax.DateProcessor: Convert timezone of datetime string to GMT.
convertToGMT(String) - Method in class org.sbml.jsbml.xml.stax.DateProcessor: Convert timezone of datetime string to GMT.
convertToGMT(Timestamp) - Method in class org.sbml.jsbml.xml.stax.DateProcessor: Convert timezone of datetime string to GMT.
convertToSI(Unit) - Static method in class org.sbml.jsbml.Unit: Returns a UnitDefinition object which contains the argument Unit converted to the appropriate SI unit.
convertToSIUnits() - Method in class org.sbml.jsbml.UnitDefinition: This method converts this unit definition to a
convertXMLNodeToString(XMLNode) - Static method in class org.sbml.jsbml.xml.XMLNode: Returns a string representation of a given XMLNode.
coord1 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
coord2 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
coord3 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
coordinate - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
coordinateBoundary - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CoordinateComponent - Class in org.sbml.jsbml.ext.spatial
CoordinateComponent() - Constructor for class org.sbml.jsbml.ext.spatial.CoordinateComponent
CoordinateComponent(CoordinateComponent) - Constructor for class org.sbml.jsbml.ext.spatial.CoordinateComponent
CoordinateComponent(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CoordinateComponent
CoordinateComponent(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CoordinateComponent
coordinateComponent - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CoordinateKind - Enum in org.sbml.jsbml.ext.spatial
CoordinateReference - Class in org.sbml.jsbml.ext.spatial: Deprecated.
Not present in spec 0.90, as be moved into DiffusionCoefficient.
CoordinateReference() - Constructor for class org.sbml.jsbml.ext.spatial.CoordinateReference: Deprecated.
CoordinateReference(CoordinateReference) - Constructor for class org.sbml.jsbml.ext.spatial.CoordinateReference: Deprecated.
coordinateReference1 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
coordinateReference2 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
coordinateSystem - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
cos(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
cos(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
cos(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
cos(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
cos(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
cosh(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
cosh(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
cosh(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
cosh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
cosh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
cot(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
cot(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
cot(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
cot(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
cot(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
cot(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the cot of n
coth(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
coth(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
coth(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
coth(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
coth(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
coth(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the coth of n
countType(ASTNode2, ASTNode.Type) - Static method in class org.sbml.jsbml.math.ASTFactory: Counts the number of nodes that have ASTNode.Type type in the tree rooted at node.
create(InputStream, boolean) - Method in interface org.sbml.jsbml.util.DocumentFactory: Creates an XML DOM document by parsing the content of the specified byte stream as XML, using a nonvalidating parser.
create(InputStream, Object[], ErrorHandler) - Method in interface org.sbml.jsbml.util.DocumentFactory: Creates an XML DOM document by parsing the content of the specified byte stream as XML, using a validating parser.
create(Reader, boolean) - Method in interface org.sbml.jsbml.util.DocumentFactory: Creates an XML DOM document by parsing the content of the specified character stream as XML, using a nonvalidating parser.
create(Reader, Object[], ErrorHandler) - Method in interface org.sbml.jsbml.util.DocumentFactory: Creates an XML DOM document by parsing the content of the specified character stream as XML, using a validating parser.
create(InputStream, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade: Creates an XML DOM document by parsing the content of the specified byte stream as XML, using a nonvalidating parser.
create(InputStream, Object[], ErrorHandler) - Method in class org.sbml.jsbml.util.JAXPFacade: Creates an XML DOM document by parsing the content of the specified byte stream as XML, using a validating parser.
create(Reader, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade: Creates an XML DOM document by parsing the content of the specified character stream as XML, using a nonvalidating parser.
create(Reader, Object[], ErrorHandler) - Method in class org.sbml.jsbml.util.JAXPFacade: Creates an XML DOM document by parsing the content of the specified character stream as XML, using a validating parser.
createAdjacentDomain() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new AdjacentDomain element and adds it to the ListOfAdjacentDomains list
createAdjacentDomain(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new AdjacentDomains element and adds it to the Geometry.listOfAdjacentDomains list
createAlgebraicRule() - Method in class org.sbml.jsbml.Model: Creates a new AlgebraicRule inside this Model and returns it.
createAnalyticGeometry() - Method in class org.sbml.jsbml.ext.spatial.Geometry
createAnalyticGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry
createAnalyticGeometry() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry
createAnalyticGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry
createAnalyticVolume() - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry: Creates a new AnalyticVolume element and adds it to the ListOfAnalyticVolumes list
createAnalyticVolume(String) - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry: Creates a new AnalyticVolume element and adds it to the ListOfAnalyticVolumes list
createAnd() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Creates a new Association element and adds it to the LogicalOperator.listOfAssociations list.
createAssignmentRule() - Method in class org.sbml.jsbml.Model: Creates a new AssignmentRule inside this Model and returns it.
createBasePoint1() - Method in class org.sbml.jsbml.ext.layout.CubicBezier: Creates, sets and returns a Point
createBasePoint1(double, double, double) - Method in class org.sbml.jsbml.ext.layout.CubicBezier: Creates, sets and returns a Point based on the given values.
createBasePoint2() - Method in class org.sbml.jsbml.ext.layout.CubicBezier: Creates, sets and returns a Point
createBasePoint2(double, double, double) - Method in class org.sbml.jsbml.ext.layout.CubicBezier: Creates, sets and returns a Point based on the given values.
createBindingSiteSpeciesType() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin: Creates a new BindingSiteSpeciesType inside this MultiModelPlugin and returns it.
createBindingSiteSpeciesType(String) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin: Creates a new BindingSiteSpeciesType inside this MultiModelPlugin and returns it.
createBoundingBox() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject: Creates and sets a BoundingBox for this object.
createBoundingBox(Dimensions) - Method in class org.sbml.jsbml.ext.layout.GraphicalObject
createBoundingBox(double, double, double) - Method in class org.sbml.jsbml.ext.layout.GraphicalObject: Creates and sets a BoundingBox for this object, with the given parameters for Dimensions.
createBoundingBox(double, double, double, double, double, double) - Method in class org.sbml.jsbml.ext.layout.GraphicalObject: Creates and sets a BoundingBox for this object, with the given parameters for Dimensions and Point.
createChangedMath() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin: Creates a new ChangedMath element and adds it to the ListOfMathChangeds list
createChangedMath(String) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin: Creates a new ChangedMath element and adds it to the ListOfMathChangeds list
createCompartment() - Method in class org.sbml.jsbml.Model: Creates a new Compartment inside this Model and returns it.
createCompartment(String) - Method in class org.sbml.jsbml.Model: Creates a new Compartment inside this Model and returns it.
createCompartmentGlyph() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new CompartmentGlyph element and adds it to the ListOfSubGlyphs list
createCompartmentGlyph(String) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new CompartmentGlyph element and adds it to the ListOfSubGlyphs list
createCompartmentGlyph(String) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates and adds a new CompartmentGlyph.
createCompartmentGlyph(String, String) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates and adds a new CompartmentGlyph.
createCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin: Creates a new CompartmentReference element and adds it to the MultiCompartmentPlugin.listOfCompartmentReferences list.
createCompartmentReference(String) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin: Creates a new CompartmentReference element and adds it to the MultiCompartmentPlugin.listOfCompartmentReferences list.
createCompartmentType() - Method in class org.sbml.jsbml.Model: Deprecated.
CompartmentTypes should no longer be used, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
createCompartmentType(String) - Method in class org.sbml.jsbml.Model: Deprecated.
CompartmentTypes should no longer be used, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
createConstraint() - Method in class org.sbml.jsbml.Model: Creates a new Constraint inside this Model and returns it.
createCoordinateComponent() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new CoordinateComponent element and adds it to the ListOfCoordinateComponents list
createCoordinateComponent(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new CoordinateComponent element and adds it to the ListOfCoordinateComponents list
createCSGeometry() - Method in class org.sbml.jsbml.ext.spatial.Geometry
createCSGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry
createCSGeometry() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry
createCSGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry
createCSGHomogeneousTransformation() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator
createCSGHomogeneousTransformation(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Creates a new CSGHomogeneousTransformation element and adds it to the ListOfCSGNodes list
createCSGObject() - Method in class org.sbml.jsbml.ext.spatial.CSGeometry: Creates a new CSGObject element and adds it to the ListOfCSGObjects list
createCSGObject(String) - Method in class org.sbml.jsbml.ext.spatial.CSGeometry: Creates a new CSGObject element and adds it to the ListOfCSGObjects list
createCSGPrimitive() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Creates a new CSGNode element and adds it to the ListOfCSGNodes list
createCSGPrimitive(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Creates a new CSGPrimitive element and adds it to the ListOfCSGNodes list
createCSGPseudoPrimitive() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator
createCSGPseudoPrimitive(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Creates a new CSGPseudoPrimitive element and adds it to the ListOfCSGNodes list
createCSGRotation() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator
createCSGRotation(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Creates a new CSGRotation element and adds it to the ListOfCSGNodes list
createCSGScale() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator
createCSGScale(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Creates a new CSGScale element and adds it to the ListOfCSGNodes list
createCSGSetOperator() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator
createCSGSetOperator(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Creates a new CSGSetOperator element and adds it to the ListOfCSGNodes list
createCSGTranslation() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator
createCSGTranslation(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Creates a new CSGTranslation element and adds it to the ListOfCSGNodes list
createCubicBezier() - Method in class org.sbml.jsbml.ext.layout.Curve: Creates a new CubicBezier instance, adds it to this Curve and returns it.
createCurve() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: Creates and adds a new Curve to this ReactionGlyph.
createCurve() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph
createCurve() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
createCurve() - Method in class org.sbml.jsbml.ext.render.RenderGroup: Creates a new RenderCurve element, adds it to the ListOfElements list and returns it.
createdDate - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
createDelay() - Method in class org.sbml.jsbml.Event: Creates a new Delay instance and sets it to this Event.
createDelay(ASTNode) - Method in class org.sbml.jsbml.Event: Creates a new Delay instance and sets it to this Event.
createDelay() - Method in class org.sbml.jsbml.Model: Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it.
createDeletion() - Method in class org.sbml.jsbml.ext.comp.Submodel: Creates a new Deletion element and adds it to the ListOfDeletions list
createDeletion(String) - Method in class org.sbml.jsbml.ext.comp.Submodel: Creates a new Deletion element and adds it to the ListOfDeletions list
createDimension() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin: Creates a new Dimension element and adds it to the ListOfDimensions list.
createDimension(String) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin: Creates a new Dimension element and adds it to the ListOfDimensions list.
createDimensions() - Method in class org.sbml.jsbml.ext.layout.BoundingBox: Creates, sets and returns a Dimensions
createDimensions(double, double, double) - Method in class org.sbml.jsbml.ext.layout.BoundingBox: Creates, sets and returns Dimensions based on the given values.
createDimensions(double, double, double) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates, sets and returns Dimensions based on the given values.
createDimensions(String, double, double, double) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates, sets and returns Dimensions based on the given values.
createDistribInput() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution: Creates a new DistribInput element and adds it to the ListOfDistribInputs list.
createDistribInput(String) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution: Creates a new DistribInput element and adds it to the ListOfDistribInputs list.
createDistribution(FunctionDefinition, String, String[], String[]) - Static method in class org.sbml.jsbml.ext.distrib.util.DistribModelBuilder: Creates the constructs needed for the given distribution in the distrib package.
createDomain() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new Domain element and adds it to the ListOfDomains list
createDomain(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new Domain element and adds it to the ListOfDomains list
createDomainType() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new DomainType element and adds it to the ListOfDomainTypes list
createDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new DomainType element and adds it to the ListOfDomainTypes list
createDrawFromDistribution() - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin: Creates and Sets a new drawFromDistribution instance.
createDynElement() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin: Creates a new DynElement element and adds it to the listOfDynElements list
createDynElement(String) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin: Creates a new DynElement element and adds it to the DynEventPlugin.getListOfDynElements().
createElement() - Method in class org.sbml.jsbml.ext.render.RenderCurve: create a new Element element and adds it to the ListOfElements list NOTE: only use this method, if ID is not mandatory in Element otherwise use @see createElement(String id)!
createElement(String) - Method in class org.sbml.jsbml.ext.render.RenderCurve: create a new Element element and adds it to the ListOfElements list
createEllipse() - Method in class org.sbml.jsbml.ext.render.RenderGroup: Creates a new Ellipse element, adds it to the ListOfElements list and returns it.
createEnd() - Method in class org.sbml.jsbml.ext.layout.CurveSegment: Creates, sets and returns an empty Point.
createEnd(double, double, double) - Method in class org.sbml.jsbml.ext.layout.CurveSegment: Creates, sets and returns a Point based on the given values.
createEnd() - Method in class org.sbml.jsbml.ext.layout.LineSegment: Creates, sets and returns a Point
createEnd(double, double, double) - Method in class org.sbml.jsbml.ext.layout.LineSegment: Creates, sets and returns a Point based on the given values.
createEvent() - Method in class org.sbml.jsbml.Model: Creates a new Event inside this Model and returns it.
createEvent(String) - Method in class org.sbml.jsbml.Model: Creates a new Event inside this Model and returns it.
createEventAssignment() - Method in class org.sbml.jsbml.Event: Creates a new EventAssignment element and adds it to the ListOfEventAssignments list.
createEventAssignment(String, ASTNode) - Method in class org.sbml.jsbml.Event: Creates a new EventAssignment element and adds it to the ListOfEventAssignments list.
createEventAssignment(Variable, ASTNode) - Method in class org.sbml.jsbml.Event: Creates a new EventAssignment element and adds it to the ListOfEventAssignments list.
createEventAssignment() - Method in class org.sbml.jsbml.Model: Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it.
createExternalModelDefinition() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin: Creates a new ExternalModelDefinition element and adds it to the ListOfExternalModelDefinitions list
createExternalModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin: Creates a new ExternalModelDefinition element and adds it to the ListOfExternalModelDefinitions list
createFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
createFluxBound(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
createFluxObjective() - Method in class org.sbml.jsbml.ext.fbc.Objective: Creates a new FluxObjective element and adds it to the ListOfFluxObjectives list
createFluxObjective(String) - Method in class org.sbml.jsbml.ext.fbc.Objective: Creates a new FluxObjective element and adds it to the ListOfFluxObjectives list
createFluxObjective(String, String) - Method in class org.sbml.jsbml.ext.fbc.Objective
createFunctionDefinition() - Method in class org.sbml.jsbml.Model: Creates a new FunctionDefinition inside this Model and returns it.
createFunctionDefinition(String) - Method in class org.sbml.jsbml.Model: Creates a new FunctionDefinition inside this Model and returns it.
createFunctionTerm() - Method in class org.sbml.jsbml.ext.qual.Transition: Creates a new instance of FunctionTerm and adds it to this Transition's Transition.listOfFunctionTerms.
createFunctionTerm(ASTNode) - Method in class org.sbml.jsbml.ext.qual.Transition: Creates a new instance of FunctionTerm with the given mathematical expression (encoded in an ASTNode) and adds it to this Transition's Transition.listOfFunctionTerms.
createGeneProduct() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Creates a new GeneProduct element and adds it to the ListOfGeneProducts list.
createGeneProduct(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Creates a new GeneProduct element and adds it to the FBCModelPlugin.listOfGeneProducts list.
createGeneProductAssociation() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
createGeneProductAssociation(String) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
createGeneProductRef() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Creates a new Association element and adds it to the LogicalOperator.listOfAssociations list.
createGeneProductRef(String) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Creates a new Association element and adds it to the LogicalOperator.listOfAssociations list.
createGeneralGlyph() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new GeneralGlyph element and adds it to the ListOfSubGlyphs list
createGeneralGlyph(String) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new GeneralGlyph element and adds it to the ListOfSubGlyphs list
createGeneralGlyph(String) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates and adds a new GeneralGlyph.
createGeneralGlyph(String, String) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates and adds a new GeneralGlyph.
createGeometry() - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin: Creates a new Geometry, adds it to this object and returns a pointer to it.
createGlobalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin: create a new GlobalRenderInformation element and adds it to the ListOfGlobalRenderInformation list NOTE: only use this method, if ID is not mandatory in GlobalRenderInformation otherwise use @see createGlobalRenderInformation(String id)!
createGlobalRenderInformation(String) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin: create a new GlobalRenderInformation element and adds it to the ListOfGlobalRenderInformation list
createGradientStop(double, String) - Method in class org.sbml.jsbml.ext.render.GradientBase: create a new GradientStop element and adds it to the ListOfGradientStops list
createGraphicalObject() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new GraphicalObject element and adds it to the ListOfSubGlyphs list
createGraphicalObject(String) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new GraphicalObject element and adds it to the ListOfSubGlyphs list
createGroup() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin: Creates a new instance of Group and add it to this GroupsModelPlugin.
createGroup(String) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin: Creates a new instance of Group and add it to this GroupsModelPlugin.
createGroup(String, String...) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin: Creates a new instance of Group and add it to this GroupsModelPlugin.
createHistory() - Method in class org.sbml.jsbml.AbstractSBase: Creates a new History and associates it with the annotation of this element.
createImage() - Method in class org.sbml.jsbml.ext.render.RenderGroup: Creates a new Image element, adds it to the ListOfElements list and returns it.
createIndex() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin: Creates a new Index element and adds it to the listOfIndices list.
createInitialAssignment() - Method in class org.sbml.jsbml.Model: Creates a new InitialAssignment inside this Model and returns it.
createInput() - Method in class org.sbml.jsbml.ext.qual.Transition
createInput(String) - Method in class org.sbml.jsbml.ext.qual.Transition
createInput(String, QualitativeSpecies, InputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Transition
createInput(String, String, InputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Transition
createInSpeciesTypeBond() - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Creates a new InSpeciesTypeBond element and adds it to the SpeciesType.listOfInSpeciesTypeBonds list.
createInSpeciesTypeBond(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Creates a new InSpeciesTypeBond element and adds it to the SpeciesType.listOfInSpeciesTypeBonds list.
createInteriorPoint() - Method in class org.sbml.jsbml.ext.spatial.Domain: Creates a new InteriorPoint element and adds it to the ListOfInteriorPoints list
createIntraSpeciesReaction() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin: Creates a new IntraSpeciesReaction inside this MultiModelPlugin and returns it.
createIntraSpeciesReaction(String) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin: Creates a new IntraSpeciesReaction inside this MultiModelPlugin and returns it.
createKineticLaw() - Method in class org.sbml.jsbml.Model: Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it.
createKineticLaw() - Method in class org.sbml.jsbml.Reaction: Creates a new KineticLaw object, installs it as this Reaction's 'kineticLaw' sub-element, and returns it.
createKineticLawParameter() - Method in class org.sbml.jsbml.Model: Creates a new local LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
createKineticParameter(String) - Method in class org.sbml.jsbml.Model: Creates a new local LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
createLayout() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin: Creates a new Layout and adds it to the current list of layouts.
createLayout(String) - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin: Creates a new Layout and adds it to the current list of layouts.
createLineSegment() - Method in class org.sbml.jsbml.ext.layout.Curve: Creates a new LineSegment instance, adds it to this Curve and returns it.
createLocalParameter() - Method in class org.sbml.jsbml.KineticLaw
createLocalParameter(String) - Method in class org.sbml.jsbml.KineticLaw
createLocalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin: create a new LocalRenderInformation element and adds it to the ListOfLocalRenderInformation list NOTE: only use this method, if ID is not mandatory in LocalRenderInformation otherwise use @see createLocalRenderInformation(String id)!
createLocalRenderInformation(String) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin: create a new LocalRenderInformation element and adds it to the ListOfLocalRenderInformation list
createMathMLDocumentFor(Node, int) - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser: Deprecated.
createMember() - Method in class org.sbml.jsbml.ext.groups.Group: Creates a new Member element and adds it to the Group.listOfMembers list.
createMember(String) - Method in class org.sbml.jsbml.ext.groups.Group: Creates a new Member element and adds it to the Group.listOfMembers list.
createMemberWithIdRef(String) - Method in class org.sbml.jsbml.ext.groups.Group: Creates a new instance of Member and add it to this Group.
createMemberWithIdRef(String, String) - Method in class org.sbml.jsbml.ext.groups.Group: Creates a new instance of Member and add it to this Group.
createMemberWithMetaIdRef(String) - Method in class org.sbml.jsbml.ext.groups.Group: Creates a new instance of Member and add it to this Group.
createMemberWithMetaIdRef(String, String) - Method in class org.sbml.jsbml.ext.groups.Group: Creates a new instance of Member and add it to this Group.
createMixedGeometry() - Method in class org.sbml.jsbml.ext.spatial.Geometry
createMixedGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
createMixedGeometry() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry
createMixedGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry: Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
createModel() - Method in class org.sbml.jsbml.SBMLDocument: Creates a new Model inside this SBMLDocument, and returns a pointer to it.
createModel(String) - Method in class org.sbml.jsbml.SBMLDocument: Creates a new instance of Model from id and the level and version of this SBMLDocument.
createModelDefinition() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin: Creates a new ModelDefinition element and adds it to the ListOfModelDefinitions list
createModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin: Creates a new ModelDefinition element and adds it to the ListOfModelDefinitions list
createModifier() - Method in class org.sbml.jsbml.Model: Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it.
createModifier(String) - Method in class org.sbml.jsbml.Model: Creates a new ModifierSpeciesReference with the specified 'id'.
createModifier() - Method in class org.sbml.jsbml.Reaction: Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it.
createModifier(Species) - Method in class org.sbml.jsbml.Reaction: Creates a new ModifierSpeciesReference, which points to the given Species, adds it to this Reaction's Reaction.listOfModifiers, and returns a pointer to it.
createModifier(String) - Method in class org.sbml.jsbml.Reaction
createModifier(String, Species) - Method in class org.sbml.jsbml.Reaction: Creates a new ModifierSpeciesReference with the given id as its identifier, which points to the given Species, adds it to this Reaction's Reaction.listOfModifiers, and returns a pointer to it.
createModifier(String, String) - Method in class org.sbml.jsbml.Reaction: Creates a new ModifierSpeciesReference with the given id as its identifier, which points to the Species with the given id, adds it to this Reaction's Reaction.listOfModifiers, and returns a pointer to it.
createNestedCVTerm() - Method in class org.sbml.jsbml.CVTerm: Creates a new CVTerm element and adds it to the CVTerm.listOfNestedCVTerms list.
createObjective() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Creates a new Objective element and adds it to the ListOfObjectives list
createObjective(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Creates a new Objective element and adds it to the ListOfObjectives list
createOr() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Creates a new Association element and adds it to the LogicalOperator.listOfAssociations list.
createOrdinalMapping() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry: Creates a new OrdinalMapping element and adds it to the ListOfOrdinalMappings list
createOutput() - Method in class org.sbml.jsbml.ext.qual.Transition
createOutput(String) - Method in class org.sbml.jsbml.ext.qual.Transition
createOutput(String, QualitativeSpecies, OutputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Transition
createOutput(String, String, OutputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Transition
createOutwardBindingSite() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin: Creates a new OutwardBindingSite element and adds it to the MultiSpeciesPlugin.listOfOutwardBindingSites list.
createParameter() - Method in class org.sbml.jsbml.Model: Creates a new Parameter inside this Model and returns it.
createParameter(String) - Method in class org.sbml.jsbml.Model: Creates a new Parameter.
createParametricGeometry() - Method in class org.sbml.jsbml.ext.spatial.Geometry
createParametricGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry
createParametricGeometry() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry
createParametricGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry
createParametricObject() - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry: Creates a new ParametricObject element and adds it to the ListOfParametricObjects list
createParametricObject(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry: Creates a new ParametricObject element and adds it to the ListOfParametricObjects list
createPlugin(String) - Method in class org.sbml.jsbml.AbstractSBase
createPlugin(String) - Method in interface org.sbml.jsbml.SBase: Creates a new SBasePlugin for the given package name or URI and adds it to this SBase.
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.ArraysParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.CompParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.DistribParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.DynParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.FBCParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.GroupsParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.L3LayoutParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.LayoutParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.MultiParser
createPluginFor(SBase) - Method in interface org.sbml.jsbml.xml.parsers.PackageParser: Creates a new SBasePlugin for the given SBase and add it to the SBasePlugin map of the SBase.
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.QualParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.RenderParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.ReqParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser
createPolygon() - Method in class org.sbml.jsbml.ext.render.RenderGroup: Creates a new Polygon element, adds it to the ListOfElements list and returns it.
createPort() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin: Creates a new Port element and adds it to the ListOfPorts list
createPort(String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin: Creates a new Port element and adds it to the ListOfPorts list
createPosition() - Method in class org.sbml.jsbml.ext.layout.BoundingBox: Creates, sets and returns a Point
createPosition(double, double, double) - Method in class org.sbml.jsbml.ext.layout.BoundingBox: Creates, sets and returns a Point based on the given values.
createPossibleSpeciesFeatureValue() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Creates a new PossibleSpeciesFeatureValue element and adds it to the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues list.
createPossibleSpeciesFeatureValue(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Creates a new PossibleSpeciesFeatureValue element and adds it to the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues list.
createPriority() - Method in class org.sbml.jsbml.Event: Creates a new, empty Priority, sets it to this Event and returns the Priority.
createPriority(ASTNode) - Method in class org.sbml.jsbml.Event: Creates a new Priority, sets it to this Event and returns it.
createProduct() - Method in class org.sbml.jsbml.Model: Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it.
createProduct(String) - Method in class org.sbml.jsbml.Model: Creates an instance of SpeciesReference and adds it to the last Reaction element that has been added to this Model.
createProduct() - Method in class org.sbml.jsbml.Reaction: Creates a new SpeciesReference, adds it to this Reaction's Reaction.listOfProducts and returns it.
createProduct(Species) - Method in class org.sbml.jsbml.Reaction: Creates a new SpeciesReference, which points to the given Species, adds it to this Reaction's Reaction.listOfProducts and returns a pointer to it.
createProduct(String) - Method in class org.sbml.jsbml.Reaction
createProduct(String, Species) - Method in class org.sbml.jsbml.Reaction: Creates a new SpeciesReference with the given id as its identifier, which points to the given Species, adds it to this Reaction's Reaction.listOfProducts and returns a pointer to it.
createProduct(String, String) - Method in class org.sbml.jsbml.Reaction
createQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.
createQualitativeSpecies(String) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.
createQualitativeSpecies(String, String, boolean) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.
createQualitativeSpecies(String, Compartment, boolean) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.
createQualitativeSpecies(String, String, Species) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Creates a new QualitativeSpecies, based on an existing Species, adds it to this QualModelPlugin and returns it.
createQualitativeSpecies(String, Compartment) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Creates a new Species inside this Model and returns it.
createRange(SBase, String, String) - Static method in class org.sbml.jsbml.ext.distrib.util.DistribModelBuilder: Creates the constructs needed for a uncertml Range.
createRateRule() - Method in class org.sbml.jsbml.Model: Creates a new RateRule inside this Model and returns it.
createReactant() - Method in class org.sbml.jsbml.Model: Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it.
createReactant(String) - Method in class org.sbml.jsbml.Model: Creates a new SpeciesReference object, with the specified 'id', for a reactant inside the last Reaction object in this Model, and returns a pointer to it.
createReactant() - Method in class org.sbml.jsbml.Reaction: Creates a new SpeciesReference, adds it to this Reaction's Reaction.listOfReactants and returns it.
createReactant(Species) - Method in class org.sbml.jsbml.Reaction: Creates a new SpeciesReference to the given Species and adds it to the Reaction.listOfReactants.
createReactant(String) - Method in class org.sbml.jsbml.Reaction: Creates a new SpeciesReference with the given identifier and adds it to this Reaction's Reaction.listOfReactants.
createReactant(String, Species) - Method in class org.sbml.jsbml.Reaction: Creates a new SpeciesReference with the given id as identifier, which points to the given Species and adds it to the Reaction.listOfReactants.
createReactant(String, String) - Method in class org.sbml.jsbml.Reaction
createReaction() - Method in class org.sbml.jsbml.Model: Creates a new Reaction inside this Model and returns it.
createReaction(String) - Method in class org.sbml.jsbml.Model: Creates a new Reaction inside this Model and returns it.
createReactionGlyph() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new ReactionGlyph element and adds it to the ListOfSubGlyphs list
createReactionGlyph(String) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new ReactionGlyph element and adds it to the ListOfSubGlyphs list
createReactionGlyph(String) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates and adds a new ReactionGlyph.
createReactionGlyph(String, String) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates and adds a new ReactionGlyph.
createRectangle() - Method in class org.sbml.jsbml.ext.render.RenderGroup: Creates a new Rectangle element, adds it to the ListOfElements list and returns it.
createReferenceGlyph() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new ReferenceGlyph element and adds it to the ListOfSubGlyphs list
createReferenceGlyph(String) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates and adds a new ReferenceGlyph
createReferenceGlyphForList() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new ReferenceGlyph element and adds it to the ListOfSubGlyphs list
createReferenceGlyphForList(String) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new ReferenceGlyph element and adds it to the ListOfSubGlyphs list
createRenderGroup() - Method in class org.sbml.jsbml.ext.render.RenderGroup: Creates a new RenderGroup element, adds it to the ListOfElements list and returns it.
createReplacedBy() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin: Creates a new ReplacedBy element and sets it in this CompSBasePlugin.
createReplacedElement() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin: Creates a new ReplacedElement element and adds it to the ListOfReplacedElements list.
createSampledField() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new SampledField element and adds it to the ListOfSampledFields list
createSampledField(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new SampledField element and adds it to the ListOfSampledFields list
createSampledFieldGeometry() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
createSampledFieldGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
createSampledFieldGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry: Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
createSampledFieldGeometryn() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry: Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
createSampledVolume() - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry: Creates a new SampledVolume element and adds it to the ListOfSampledVolumes list
createSampledVolume(String) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry: Creates a new SampledVolume element and adds it to the ListOfSampledVolumes list
createSBaseRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Creates a new SBaseRef instance and add it to this SBaseRef
createSpatialComponent() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin: Creates a new SpatialComponent element and adds it to the listOfSpatialComponents list
createSpatialComponent(String) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin: Creates a new SpatialComponent element and adds it to the DynCompartmentPlugin.getListOfSpatialComponents()
createSpecies() - Method in class org.sbml.jsbml.Model: Creates a new Species inside this Model and returns it.
createSpecies(String) - Method in class org.sbml.jsbml.Model: Creates a new Species inside this Model and returns it.
createSpecies(String, Compartment) - Method in class org.sbml.jsbml.Model: Creates a new Species inside this Model and returns it.
createSpecies(String, String, Compartment) - Method in class org.sbml.jsbml.Model: Creates a new Species inside this Model and returns it.
createSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin: Creates a new SpeciesFeature element and adds it to the MultiSpeciesPlugin.listOfSpeciesFeatures list.
createSpeciesFeature(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin: Creates a new SpeciesFeature element and adds it to the MultiSpeciesPlugin.listOfSpeciesFeatures list.
createSpeciesFeatureChange() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Creates a new SpeciesFeatureChange element and adds it to the SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges list.
createSpeciesFeatureChange(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Creates a new SpeciesFeatureChange element and adds it to the SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges list.
createSpeciesFeatureType() - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Creates a new SpeciesFeatureType element and adds it to the SpeciesType.listOfSpeciesFeatureTypes list.
createSpeciesFeatureType(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Creates a new SpeciesFeatureType element and adds it to the SpeciesType.listOfSpeciesFeatureTypes list.
createSpeciesFeatureValue() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature: Creates a new SpeciesFeatureValue element and adds it to the SpeciesFeature.listOfSpeciesFeatureValues list.
createSpeciesGlyph() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new SpeciesGlyph element and adds it to the ListOfSubGlyphs list
createSpeciesGlyph(String) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new SpeciesGlyph element and adds it to the ListOfSubGlyphs list
createSpeciesGlyph(String) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates and adds a new SpeciesGlyph with the given identifier.
createSpeciesGlyph(String, String) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates and adds a new SpeciesGlyph.
createSpeciesReferenceGlyph() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new SpeciesReferenceGlyph element and adds it to the ListOfSubGlyphs list
createSpeciesReferenceGlyph(String) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new SpeciesReferenceGlyph element and adds it to the ListOfSubGlyphs list
createSpeciesReferenceGlyph(String) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: Creates and adds a new SpeciesReferenceGlyph
createSpeciesReferenceGlyph(String, String) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: Creates and adds a new SpeciesReferenceGlyph
createSpeciesType() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin: Creates a new SpeciesType inside this MultiModelPlugin and returns it.
createSpeciesType(String) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin: Creates a new SpeciesType inside this MultiModelPlugin and returns it.
createSpeciesType() - Method in class org.sbml.jsbml.Model: Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
createSpeciesType(String) - Method in class org.sbml.jsbml.Model: Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
createSpeciesTypeComponentIndex() - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Creates a new SpeciesTypeComponentIndex element and adds it to the SpeciesType.listOfSpeciesTypeComponentIndexes list.
createSpeciesTypeComponentIndex(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Creates a new SpeciesTypeComponentIndex element and adds it to the SpeciesType.listOfSpeciesTypeComponentIndexes list.
createSpeciesTypeComponentMapInProduct() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin: Creates a new SpeciesTypeComponentMapInProduct element and adds it to the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts list.
createSpeciesTypeInstance() - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Creates a new SpeciesTypeInstance element and adds it to the SpeciesType.listOfSpeciesTypeInstances list.
createSpeciesTypeInstance(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Creates a new SpeciesTypeInstance element and adds it to the SpeciesType.listOfSpeciesTypeInstances list.
createStart() - Method in class org.sbml.jsbml.ext.layout.CurveSegment: Creates, sets and returns an empty Point.
createStart(double, double, double) - Method in class org.sbml.jsbml.ext.layout.CurveSegment: Creates, sets and returns a Point based on the given values.
createStart() - Method in class org.sbml.jsbml.ext.layout.LineSegment: Creates, sets and returns a Point
createStart(double, double, double) - Method in class org.sbml.jsbml.ext.layout.LineSegment: Creates, sets and returns a Point based on the given values.
createStatisticsCollection(SBase, String[], String[], String[]) - Static method in class org.sbml.jsbml.ext.distrib.util.DistribModelBuilder: Creates the constructs needed for a StatisticsCollection.
createStatisticsCollection(SBase, String[], String[], String[], String[], String[]) - Static method in class org.sbml.jsbml.ext.distrib.util.DistribModelBuilder: Creates the constructs needed for a StatisticsCollection.
createStoichiometryMath(ASTNode) - Method in class org.sbml.jsbml.SpeciesReference: Deprecated.
since SBML Level 3 this should not be used anymore.
createSubmodel() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin: Creates a new Submodel element and adds it to the ListOfSubmodels list
createSubmodel(String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin: Creates a new Submodel element and adds it to the ListOfSubmodels list
createText() - Method in class org.sbml.jsbml.ext.render.RenderGroup: Creates a new Text element, adds it to the ListOfElements list and returns it.
createTextGlyph() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new TextGlyph element and adds it to the ListOfSubGlyphs list
createTextGlyph(String) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Creates a new TextGlyph element and adds it to the ListOfSubGlyphs list
createTextGlyph(String) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates and adds a new TextGlyph.
createTextGlyph(String, String) - Method in class org.sbml.jsbml.ext.layout.Layout: Creates and adds a new TextGlyph.
createTransition() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Creates a new Transition inside this QualModelPlugin and returns it.
createTransition(String) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Creates a new Transition inside this QualModelPlugin and returns it.
createTransition(String, Input, Output) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Creates a new Transition inside this QualModelPlugin and returns it.
createTrigger() - Method in class org.sbml.jsbml.Event: Creates a new Trigger instance and sets it to this Event.
createTrigger(boolean, boolean) - Method in class org.sbml.jsbml.Event: Creates a new Trigger instance and sets it to this Event.
createTrigger(boolean, boolean, ASTNode) - Method in class org.sbml.jsbml.Event: Creates a new Trigger instance and sets it to this Event.
createTrigger(ASTNode) - Method in class org.sbml.jsbml.Event: Creates a new Trigger instance and sets it to this Event.
createTrigger() - Method in class org.sbml.jsbml.Model: Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it.
createUncertainty() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin: Creates and Sets a new Uncertainty instance.
createUnit() - Method in class org.sbml.jsbml.Model: Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.
createUnit(Unit.Kind) - Method in class org.sbml.jsbml.Model: Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.
createUnit() - Method in class org.sbml.jsbml.UnitDefinition
createUnit(Unit.Kind) - Method in class org.sbml.jsbml.UnitDefinition
createUnitDefinition() - Method in class org.sbml.jsbml.Model: Creates a new UnitDefinition inside this Model and returns it.
createUnitDefinition(String) - Method in class org.sbml.jsbml.Model: Creates a new UnitDefinition inside this Model and returns it.
Creator - Class in org.sbml.jsbml: Contains all the information about a creator of a Model (or other SBase in level 3).
Creator() - Constructor for class org.sbml.jsbml.Creator: Creates a Creator instance.
Creator(Creator) - Constructor for class org.sbml.jsbml.Creator: Creates a Creator instance from a given Creator.
Creator(String, String, String, String) - Constructor for class org.sbml.jsbml.Creator: Creates a Creator instance.
creator - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
csc(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
csc(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
csc(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
csc(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
csc(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
csc(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the csc of n
csch(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
csch(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
csch(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
csch(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
csch(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
csch(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the csch of n
CSGeometry - Class in org.sbml.jsbml.ext.spatial
CSGeometry() - Constructor for class org.sbml.jsbml.ext.spatial.CSGeometry
CSGeometry(CSGeometry) - Constructor for class org.sbml.jsbml.ext.spatial.CSGeometry
CSGeometry(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGeometry
CSGeometry(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGeometry
csGeometry - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CSGHomogeneousTransformation - Class in org.sbml.jsbml.ext.spatial
CSGHomogeneousTransformation() - Constructor for class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation
CSGHomogeneousTransformation(CSGHomogeneousTransformation) - Constructor for class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation
CSGHomogeneousTransformation(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation
CSGHomogeneousTransformation(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation
csgHomogeneousTransformation - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CSGNode - Class in org.sbml.jsbml.ext.spatial
CSGNode() - Constructor for class org.sbml.jsbml.ext.spatial.CSGNode
CSGNode(CSGNode) - Constructor for class org.sbml.jsbml.ext.spatial.CSGNode
CSGNode(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGNode
CSGNode(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGNode
csgNode - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CSGObject - Class in org.sbml.jsbml.ext.spatial
CSGObject() - Constructor for class org.sbml.jsbml.ext.spatial.CSGObject
CSGObject(CSGObject) - Constructor for class org.sbml.jsbml.ext.spatial.CSGObject
CSGObject(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGObject
CSGObject(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGObject
CSGPrimitive - Class in org.sbml.jsbml.ext.spatial
CSGPrimitive() - Constructor for class org.sbml.jsbml.ext.spatial.CSGPrimitive
CSGPrimitive(CSGPrimitive) - Constructor for class org.sbml.jsbml.ext.spatial.CSGPrimitive
CSGPrimitive(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGPrimitive
CSGPrimitive(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGPrimitive
csgPrimitive - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CSGPseudoPrimitive - Class in org.sbml.jsbml.ext.spatial
CSGPseudoPrimitive() - Constructor for class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive
CSGPseudoPrimitive(CSGPseudoPrimitive) - Constructor for class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive
CSGPseudoPrimitive(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive
CSGPseudoPrimitive(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive
csgPseudoPrimitive - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CSGRotation - Class in org.sbml.jsbml.ext.spatial
CSGRotation() - Constructor for class org.sbml.jsbml.ext.spatial.CSGRotation
CSGRotation(CSGRotation) - Constructor for class org.sbml.jsbml.ext.spatial.CSGRotation
CSGRotation(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGRotation
CSGRotation(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGRotation
csgRotation - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CSGScale - Class in org.sbml.jsbml.ext.spatial
CSGScale() - Constructor for class org.sbml.jsbml.ext.spatial.CSGScale
CSGScale(CSGScale) - Constructor for class org.sbml.jsbml.ext.spatial.CSGScale
CSGScale(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGScale
CSGScale(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGScale
csgScale - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CSGSetOperator - Class in org.sbml.jsbml.ext.spatial
CSGSetOperator() - Constructor for class org.sbml.jsbml.ext.spatial.CSGSetOperator
CSGSetOperator(CSGSetOperator) - Constructor for class org.sbml.jsbml.ext.spatial.CSGSetOperator
CSGSetOperator(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGSetOperator
CSGSetOperator(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGSetOperator
csgSetOperator - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CSGTransformation - Class in org.sbml.jsbml.ext.spatial
CSGTransformation() - Constructor for class org.sbml.jsbml.ext.spatial.CSGTransformation
CSGTransformation(CSGTransformation) - Constructor for class org.sbml.jsbml.ext.spatial.CSGTransformation
CSGTransformation(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGTransformation
CSGTransformation(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGTransformation
csgTransformation - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CSGTranslation - Class in org.sbml.jsbml.ext.spatial
CSGTranslation() - Constructor for class org.sbml.jsbml.ext.spatial.CSGTranslation
CSGTranslation(CSGTranslation) - Constructor for class org.sbml.jsbml.ext.spatial.CSGTranslation
CSGTranslation(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGTranslation
CSGTranslation(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.CSGTranslation
csgTranslation - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
CubicBezier - Class in org.sbml.jsbml.ext.layout: In order to be able to represent smooth curves the Layout package defines the class CubicBezier.
CubicBezier() - Constructor for class org.sbml.jsbml.ext.layout.CubicBezier
CubicBezier(CubicBezier) - Constructor for class org.sbml.jsbml.ext.layout.CubicBezier
CubicBezier(int, int) - Constructor for class org.sbml.jsbml.ext.layout.CubicBezier
currentToken - Variable in exception org.sbml.jsbml.math.parser.ParseException: This is the last token that has been consumed successfully.
currentToken - Variable in exception org.sbml.jsbml.text.parser.ParseException: This is the last token that has been consumed successfully.
Curve - Class in org.sbml.jsbml.ext.layout: The Curve class describes how to connect elements in a diagram defined with the use of the Layout package.
Curve() - Constructor for class org.sbml.jsbml.ext.layout.Curve
Curve(Curve) - Constructor for class org.sbml.jsbml.ext.layout.Curve
Curve(int, int) - Constructor for class org.sbml.jsbml.ext.layout.Curve
curve - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
CurveSegment - Class in org.sbml.jsbml.ext.layout: Parent class to LineSegment and CubicBezier.
CurveSegment() - Constructor for class org.sbml.jsbml.ext.layout.CurveSegment
CurveSegment(CurveSegment) - Constructor for class org.sbml.jsbml.ext.layout.CurveSegment
CurveSegment(int, int) - Constructor for class org.sbml.jsbml.ext.layout.CurveSegment
curveSegment - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
CurveSegment.Type - Enum in org.sbml.jsbml.ext.layout
CUSTOM_RDF - Static variable in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser: A Constant String that is used to store any remaining children or attributes after having removed the standard SBML RDF elements and attributes.
CVTerm - Class in org.sbml.jsbml: Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element of a SBML component.
CVTerm() - Constructor for class org.sbml.jsbml.CVTerm: Creates a CVTerm instance.
CVTerm(CVTerm) - Constructor for class org.sbml.jsbml.CVTerm: Creates a CVTerm instance from a given CVTerm.
CVTerm(CVTerm.Qualifier, String...) - Constructor for class org.sbml.jsbml.CVTerm: Guesses the CVTerm.Type argument and sets the CVTerm.Qualifier attribute appropriately.
CVTerm(CVTerm.Type, CVTerm.Qualifier, String...) - Constructor for class org.sbml.jsbml.CVTerm: Creates a new CVTerm with the given CVTerm.Type and CVTerm.Qualifier pointing to all given resources.
CVTerm(XMLNode) - Constructor for class org.sbml.jsbml.CVTerm
CVTerm.Qualifier - Enum in org.sbml.jsbml: This enum list all the possible MIRIAM qualifiers.
CVTerm.Type - Enum in org.sbml.jsbml: This enum list all the possible MIRIAM qualifiers type.
CVTermFilter - Class in org.sbml.jsbml.util.filters: This filter accepts only instances of CVTerm with a certain content or instances of SBase that are annotated with appropriate CVTerm objects.
CVTermFilter() - Constructor for class org.sbml.jsbml.util.filters.CVTermFilter
CVTermFilter(CVTerm.Qualifier) - Constructor for class org.sbml.jsbml.util.filters.CVTermFilter
CVTermFilter(CVTerm.Qualifier, String) - Constructor for class org.sbml.jsbml.util.filters.CVTermFilter
cx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
cy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
cz - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

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